Workflow: umi molecular alignment workflow

Fetched 2023-01-10 02:17:29 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs target_intervals target_intervals qc Exome QC workflow target_intervals->qc target_intervals alignment umi molecular alignment workflow target_intervals->alignment target_intervals read_structure read_structure read_structure->alignment read_structure bam bam bam->alignment bam reference reference reference->qc reference reference->alignment reference sample_name sample_name sample_name->alignment sample_name per_target_intervals per_target_intervals per_target_intervals->qc per_target_intervals summary_intervals summary_intervals summary_intervals->qc summary_intervals picard_metric_accumulation_level picard_metric_accumulation_level picard_metric_accumulation_level->qc picard_metric_accumulation_level minimum_base_quality minimum_base_quality minimum_base_quality->qc minimum_base_quality minimum_mapping_quality minimum_mapping_quality minimum_mapping_quality->qc minimum_mapping_quality bait_intervals bait_intervals bait_intervals->qc bait_intervals per_base_intervals per_base_intervals per_base_intervals->qc per_base_intervals omni_vcf omni_vcf omni_vcf->qc omni_vcf alignment_summary_metrics alignment_summary_metrics verify_bam_id_depth verify_bam_id_depth hs_metrics hs_metrics per_base_coverage_metrics per_base_coverage_metrics verify_bam_id_metrics verify_bam_id_metrics insert_size_histogram insert_size_histogram per_target_hs_metrics per_target_hs_metrics duplex_seq_metrics duplex_seq_metrics summary_hs_metrics summary_hs_metrics adapter_histogram adapter_histogram per_base_hs_metrics per_base_hs_metrics insert_size_metrics insert_size_metrics per_target_coverage_metrics per_target_coverage_metrics aligned_bam aligned_bam flagstats flagstats qc->alignment_summary_metrics qc->verify_bam_id_depth qc->hs_metrics qc->per_base_coverage_metrics qc->verify_bam_id_metrics qc->insert_size_histogram qc->per_target_hs_metrics qc->summary_hs_metrics qc->per_base_hs_metrics qc->insert_size_metrics qc->per_target_coverage_metrics qc->flagstats alignment->duplex_seq_metrics alignment->adapter_histogram alignment->aligned_bam alignment->qc bam
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Inputs

ID Type Title Doc
bam File[]
omni_vcf File
reference String
sample_name String
bait_intervals File
read_structure String[]
target_intervals File
summary_intervals https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/types/labelled_file.yml#labelled_file[]
minimum_base_quality Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/types/labelled_file.yml#labelled_file[]
minimum_mapping_quality Integer (Optional)
picard_metric_accumulation_level String

Steps

ID Runs Label Doc
qc
qc_exome.cwl (Workflow)
Exome QC workflow
alignment umi molecular alignment workflow

Outputs

ID Type Label Doc
flagstats File
hs_metrics File
aligned_bam File
adapter_histogram File[]
duplex_seq_metrics File[]
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
verify_bam_id_depth File
insert_size_histogram File
per_target_hs_metrics File[]
verify_bam_id_metrics File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
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Permalink: https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/subworkflows/molecular_qc.cwl